<div class='content'>

	<h2>项目描述</h2>

	<h3>时间表(45*2+10=100min)</h3>
	<p style="font-family:monospace; white-space: pre;">上午: 8:00-9:40; 10:00-11:40;		下午: 1:40-3:20; 3:40- 5:20; 		晚上: 7:00-8:40; 8:50-10:30;</p>
	<pre class=saying>盛年难再来，一日难再晨。及时当勉励，岁月不待人。 —— 陶渊明</pre>




	<h3>R语言基础</h3>
	<pre class=saying>学习一门编程语言最快的方法就是阅读源代码。</pre>

	<p>
		<a target="_blank" href="https://www.r-project.org">R语言</a>是一个自由软件环境，主要用于统计、可视化。支持多种平台。我们主要学习R语言语法、R定义的文件、R包、可视化等。
		R语言小抄：
		<a target="_blank" href="https://cran.r-project.org/doc/contrib/Short-refcard.pdf">Short-refcard.pdf(2004)</a>|
		<a target="_blank" href="https://cran.r-project.org/doc/contrib/Liu-R-refcard.pdf">(中文版2008)</a>, 
		<a target="_blank" href="https://cran.r-project.org/doc/contrib/Baggott-refcard-v2.pdf">Baggott-refcard-v2.pdf(2012)</a>,
	</p>

	<p>入门教程: 
		<a target="_blank" href='https://cran.r-project.org/doc/manuals/'>R manuals</a> | 
		<a target="_blank" href='https://www.cyclismo.org/tutorial/R/index.html'>R 基础</a> | 
		<a target="_blank" href='https://cran.r-project.org/doc/manuals/R-FAQ.html'>R-FAQ</a> | 
		<a target="_blank" href='https://cran.r-project.org/doc/manuals/R-admin.html' title="安装R和R包">R-admin</a> | 
		<a target="_blank" href='https://cran.r-project.org/doc/manuals/R-intro.html' title="R简介">R-intro</a> | 
		<a target="_blank" href='https://cran.r-project.org/doc/manuals/R-data.html' title="R数据的IO">R-data</a> | 
		<a target="_blank" href='https://cran.r-project.org/doc/manuals/R-lang.html' title="R语言定义 OOP" class="button pink">R-lang</a> | 
		<a target="_blank" href='https://openbiox.github.io/Cookbook-for-R-Chinese/' title="中文版">Cookbook-for-R</a> | 
		<a target="_blank" href='http://applied-r.com/applied-r-about/' title="R 应用者">Applied R Code</a> | 
	</p>
	<p>
		<b class=red>高级教程</b>: 
		<a target="_blank" href='https://cran.r-project.org/doc/manuals/R-ints.html' title="R内部构件及R的内部编码标准 S4对象 src/main">R-ints</a> | 
		<a target="_blank" href='https://cran.r-project.org/doc/manuals/R-exts.html' title="如何写R包等扩展">R-exts</a> | 
		<a target="_blank" href='https://cran.r-project.org/doc/manuals/fullrefman.pdf' title="Reference Index(近4千页)">fullRefMan</a> | 
		<a target="_blank" href='http://adv-r.had.co.nz/' title="高级R编程">adv R</a> | 
		<a target="_blank" href='http://datasciencefree.com/advancedR.pdf' title="高级R编程" class="button pink">adv R概要</a> | 
		<a target="_blank" href='https://cran.r-project.org/web/views/' title="与某任务相关的R包">CRAN Task Views</a> | 
		<a target="_blank" href='https://www.zhihu.com/people/shou-hu-tian-xin-67/posts?page=3' title="grid包" class="button pink">grid包</a> | 
		<a target="_blank" href='https://bookdown.org/rdpeng/RProgDA/the-grid-package.html#viewports' title="Mastering Software Development in R">grid包(en)</a> | 
		<a target="_blank" href='https://bookdown.org/' title="R生成电子书" class="button pink">bookdown.org</a> | 
		<a target="_blank" href='https://www.jottr.org/' title="做 R 并发/多线程的大佬， future 包的作者的博客">并发/多线程</a> | 
	</p>

	<p>	
		<b class=red>开发者</b>: 
		<a target="_blank" href='https://developer.r-project.org/Blog/public/index.html' title="R核心">R核心开发者博客</a> | 
		<a target="_blank" href='https://r-pkgs.org/namespace.html' title="R核心">动物书-R包开发</a> | 
		<a target="_blank" href='http://jmonlong.github.io/Hippocamplus/r/#rcpp' title="Rcpp">Rcpp 笔记(精炼半页)</a> | 
		<a target="_blank" href='https://rstats.wtf/' title="What They Forgot to Teach You About R(如何调试)">没人教的R知识</a> | 
		<a target="_blank" href='https://contributions.bioconductor.org/debugging-cc-code.html' title="bioconductor维护的文档: 如何开发、维护和同行评审R包">bioconductor 调试C/C++</a> | 
	</p>
	<p>	
		<b class=red>电子书</b>: 
		<a target="_blank" href='https://csgillespie.github.io/efficientR/' title="R核心">Efficient R programming</a> | 
		<a target="_blank" href='https://bookdown.org/MathiasHarrer/Doing_Meta_Analysis_in_R/discovering-R.html'>Meta 分析</a> | 
		<a target="_blank" href='https://compgenomr.github.io/book/' class="button green">Computational Genomics with R(计算基因组学)</a> | 
		<a target="_blank" href="https://dawneve.github.io/R_best_practice/" class="button blue">我写的《R 语言最佳实践》</a> | 
	</p>






	<h3>R语言画图</h3>
	<p><b>News</b>: 
		<a target="_blank" href='https://www.r-bloggers.com/'>r-bloggers</a> | 
		<a target="_blank" href='http://hadley.nz/'> Hadley Wickham 个人主页</a> auther of ggplot2, dplyr, ... | 
		<a target="_blank" href="https://www.rstudio.com/wp-content/uploads/2015/08/ggplot2-cheatsheet.pdf">ggplot2-cheatsheet.pdf(2015)</a>,
	</p>






	<h3>R语言与统计学</h3>
	<pre class=saying>数据和特征决定了效果上限，模型和算法决定了逼近这个上限的程度。</pre>
	<p>R统计学教程 <a target="_blank" href="http://www.r-tutor.com/">r-tutor</a>: 
		<a target="_blank" href='http://www.r-tutor.com/elementary-statistics/interval-estimation/interval-estimate-population-mean-known-variance'> Z-test</a> | 
		<a target="_blank" href='https://www.math.pku.edu.cn/teachers/lidf/docs/Rbook/html/_Rbook/stat-basics.html' class="button pink">R 统计学(PKU教程)</a> | 
	</p>


	<p>斯坦福生物统计课程(bios221): 
		<a target="_blank" href='https://web.stanford.edu/class/bios221/book/09-chap.html'>2024</a> | 
		
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Rfiles/'>Rfiles</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/introduction.html'>Introduction</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Generative.html'>1 Generative Models for Discrete Data</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Models.html'>2 Statistical Modeling</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Graphics.html'>3 High Quality Graphics in R</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Mixtures.html' title="(VST)variance-stabilizing transformations ">4 Mixture Models</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Clustering.html'>5 Clustering</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Testing.html'>6 Testing</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Multivariate.html'>7 Multivariate Analysis</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-CountData.html'>8 High-Throughput Count Data</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-MultivaHetero.html'>9 Multivariate methods for heterogeneous data</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Graphs.html'>10 Networks and Trees</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Images.html'>11 Image data</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Supervised.html'>12 Supervised Learning</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/Chap-Design.html'>13 Design of High Throughput Experiments and their Analyses</a> | 
		<a target="_blank" href='http://web.stanford.edu/class/bios221/book/statistical-concordance.html'>Statistical Concordance</a> | 
	</p>





	<hr />


	<p>	
		<a target="_blank" href='https://www.rstudio.com'> RStudio</a> makes R easier to use. It includes a code editor, debugging & visualization tools.	| 
		<a target="_blank" href='https://www.rstudio.com/wp-content/uploads/2015/02/rmarkdown-cheatsheet.pdf'>rmarkdown-cheatsheet.pdf</a> | 
		<a target="_blank" href='https://rstudio.com/resources/cheatsheets/'>More cheatsheets</a> | 
		<a target="_blank" href='https://github.com/rstudio/cheatsheets/' title="another url">cheatsheets@github</a> | 
	</p>




	<p>	<a target="_blank" href='https://mran.revolutionanalytics.com/'> RevolutionAnalytics</a> R is the world’s most powerful programming language for statistical computing, machine learning and graphics and has a thriving global community of users, developers and contributors. <a target="_blank" href="https://mran.revolutionanalytics.com/timemachine">[CRAN Time Machine]</a> For the purpose of reproducibility, MRAN hosts daily snapshots of the CRAN R packages and R releases as far back as Sept. 17, 2014. | <a target="_blank" href='https://mran.microsoft.com/snapshot/2018-01-12/bin/windows/contrib/3.4/'> R包3.4版本 </a></p>

	<p> <a target="_blank" href='https://www.bioconductor.org'> Bioconductor</a> provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1560 software packages, and an active user community. Bioconductor is also available as an AMI (Amazon Machine Image) and a series of <a target="_blank" href="http://www.bioconductor.org/help/docker/">Docker</a> images.</p>




	<hr />
	<p>	<a target="_blank" href='https://zhuanlan.zhihu.com/Data-AnalysisR'> Data-AnalysisR知乎专栏</a> R及周边知识点  MongoDB, ggplot2, R原生绘图, </p>
	<p>常用的R包list: 数据处理、机器学习、可视化、地图、聚类、统计、优化<a target="_blank" href='https://www.cnblogs.com/zongfa/p/8537058.html'> 推荐1 </a>， <a target="_blank" href='https://support.rstudio.com/hc/en-us/articles/201057987-Quick-list-of-useful-R-packages'> 推荐2 </a> </p>







	<h2>R语言资源</h2>
	<p>R官方资源：
		<a target="_blank" class='button blue' href='http://cran.r-project.org/mirrors.html'> CRAN 镜像</a>
		| 
		<a target="_blank" class='button red' href='https://cran.r-project.org/manuals.html'>Manuals</a>
		<a target="_blank" class='button red' href='https://www.r-project.org/other-docs.html'>Documentation</a>
		<a target="_blank" class='button red' href='https://www.r-project.org/help.html'>R帮助</a>
		<a target="_blank" class='button red' href='http://r.789695.n4.nabble.com/R-help-f789696.html'>R邮件组论坛</a>
	</p>



	<p>cran.r-project.org R包：
		 <a target="_blank" class='button red' href='https://cran.r-project.org/web/packages/plyr/' title="plyr: Tools for Splitting, Applying and Combining Data">plyr 包</a>
		 <a target="_blank" class='button red' href='http://had.co.nz/plyr/' title="The split-apply-combine strategy for R">plyr site</a> |
			<a target="_blank" class='button red' href='https://cran.r-project.org/web/packages/ggplot2/index.html'>ggplot2 包</a> |
	</p>





	<p>R语言权威教材：
		 <a target="_blank" class='button orange' href='https://www.statmethods.net/' title="Quick R 网站">《R语言实战(中文完整版)》 R in Action</a> |
		 <a target="_blank" class='button orange' href='http://adv-r.had.co.nz/' title="Adv R 网站">Advanced R(V1)</a> helps you master R as a programming language, teaching you what makes R tick. |
		 <a target="_blank" class='button orange' href='https://adv-r.hadley.nz/' title="Adv R 网站v2">Advanced R(V2)</a> The book is designed primarily for R users who want to improve their programming skills and understanding of the language. |
		 <a target="_blank" class='button orange' href='http://r4ds.had.co.nz/' title="Adv R 网站">R for Data Science</a>  with Garrett Grolemund, introduces the key tools for doing data science with R. |
		 <a target="_blank" class='button orange' href='http://www.cookbook-r.com' title="Adv R 网站">Cookbook for R</a> The goal of the cookbook is to provide solutions to common tasks and problems in analyzing data. |
		 <a target="_blank" class='button orange' href='https://www.manning.com/books/practical-data-science-with-r-second-edition?gclid=EAIaIQobChMIld-xoMzq4QIVkbuWCh20HgRgEAEYASAFEgL3bPD_BwE' title="Free">Practical Data Science with R, 2nd Edition</a> A detailed, well explained book to the real life practice of data science techniques.|
		 <a target="_blank" class='button orange' href='http://shop.oreilly.com/product/9781593273842.do' title="豆瓣 https://book.douban.com/subject/24699632/">R语言编程艺术</a> The Art of R Programming: A Tour of Statistical Software Design |
		 <a target="_blank" class='button orange' href='https://www.oreilly.com/library/view/r-in-a/9781449358204/'>R in a Nutshell, 2nd Edition</a> a complete desktop reference to R |

	</p>





	<p>R语言论坛：
		 <a target="_blank" href='http://bbs.pinggu.org/forum-69-1.html' title="经管之家">经管之家论坛</a> | 
		 <a target="_blank" href='https://stats.idre.ucla.edu/r/' title="Institute for Digital Research and Education">R @ ucla.edu</a> |
		 <a target="_blank" class='button green' href='https://www.r-graph-gallery.com/' title="hundreds of distinctive graphics made with the R programming language, always with the reproducible code snippet">R graph gallery</a> |
		 <a target="_blank" class='button green' href='http://www.sthda.com/english/wiki/ggplot2-essentials' title="The concept behind ggplot2 divides plot into three different fundamental parts: Plot = data + Aesthetics + Geometry.">ggplot2-essentials</a> |
		 <a target="_blank" class='button green' href='http://www.sthda.com/english/wiki/data-visualization' title="R Base Graphs-Lattice Graphs-ggplot2-3D Graphics">R Data Visualization</a> |
	</p>









	<h2>R 包管理</h2>
<!--
		 <a target="_blank" href='xx' title="">xx</a> | 
-->
	<p><a target="_blank" href='https://ropensci.org/r-universe/' title="">The R-universe system</a> The R-universe platform is a new umbrella project under which we experiment with various new ideas for improving publication and discovery of research software in R.

The system consists of several components and subprojects, that come together on the front-end dashboard on <a target="_blank" href='https://r-universe.dev'>https://r-universe.dev</a>  | 
	</p>





<h3>R包 国内镜像</h3>
<pre>
https://mirrors.sjtug.sjtu.edu.cn/cran/web/packages/

# install pkg ----
#使用命令行设置镜像
options()$repos
## 查看使用install.packages安装时的默认镜像
options()$BioC_mirror 

##查看使用bioconductor的默认镜像
options(BioC_mirror="https://mirrors.ustc.edu.cn/bioc/") #镜像为空，不能用 #指定镜像，中国科技大学镜像
options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor/")

options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/")) #指定install.packages安装镜像，清华镜像


# 安装示例
install.packages("pheatmap")
install.packages("BiocManager")
install.packages("ggplot2")
install.packages("Seurat")

#BioConductor 的包
if (!requireNamespace("devtools"))
    install.packages("devtools")
devtools::install_github("TomKellyGenetics/leiden")
</pre>


<h3>进一步学习</h3>
<pre>
<b>R for Data Science (Grolemund and Wickham 2016)</b>, a free book introducing many concepts and ‘tidy’ packages for working with data (a free online version is available from r4ds.had.co.nz/).

<b>R programming for Data Science (Peng 2014)</b>, which provides in depth coverage of analysis and visualisation of datasets.
	https://leanpub.com/rprogramming

<b>Advanced R Programming (H. Wickham 2014a)</b>, an advanced book which looks at the internals of how R works (free from adv-r.had.co.nz).
</pre>






<pre>
“那是一份高质量的R代码，各种标准的向量化操作、匿名函数、优美的代码格式让我欣喜，也让我茫然。”

https://github.com/paul-shannon/learningR
</pre>

</div>
